Description

This function converts an initial data vector named by non-entrez ids to the same
vector but with entrez ids, and vice versa. Genes for which no mapping were found
will be removed. This function can also take a matrix, with gene identifiers as
row names.

Usage

1
2

Arguments

geneList

a named integer or numeric vector, or a matrix with rows named by gene
identifiers

initialIDs

a single character value specifying the type of initial identifiers for
input 'geneList'. The current version can take one of the following types:
"Ensembl.transcript", "Ensembl.prot", "Ensembl.gene", "Entrez.gene",
"RefSeq", "Symbol", "GenBank" and "wormbase"

finalIDs

a single character value specifying the type of final identifiers to
which users want to convert. The current version can take one of the following
types: "Ensembl.transcript", "Ensembl.prot", "Ensembl.gene", "Entrez.gene",
"RefSeq", "Symbol", "GenBank" and "wormbase"

keepMultipleMappings

a single logical value. If TRUE, the function keeps the entries with
multiple mappings (first mapping is kept). If FALSE, the entries with
multiple mappings will be discarded.

verbose

a single logical value specifying to display detailed messages (when
verbose=TRUE) or not (when verbose=FALSE)

Details

This function relies on the org.Ce.eg.db package and therefore only maps

from any identifier to an Entrez gene id, or

from an Entrez gene ID to any identifier

The entries that could not be mapped to any identifiers are removed from
the resulting data vector/matrix.

Value

the same vector/matrix but with names/rownames corresponding to a
different type of identifiers